Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands.
The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema.
The second takes an h5ad and checks if it follows the schema version written into its metadata.
Both are currently marked as "experimental" as the primary intended users are still at CZI.
This PR contains a refactoring to make adding new features easier.
The new features include supporting the tiledb format, and the multi dataset application.
The refactoring includes
Simplifying the directory structure and files.
a class structure to handle annotations (currently one type: AnnotationsLocalFile).
a class to handle application configuration
a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb.
Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface.
The multi dataset option is not fully supported yet, and so the option to use it is hidden.
Use "cli launch --dataroot ..."
To access this feature.
All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
